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A couple path changes due to storage relocation on Yale Farnam cluster #13

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Merged
merged 1 commit into from
Sep 16, 2020
Merged

A couple path changes due to storage relocation on Yale Farnam cluster #13

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2 changes: 1 addition & 1 deletion src/shell/cmfinder_source_template.sh
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
# Replace path below with the location of the cmfinder executables on your compute cluster
export PATH=$PATH:/ysm-gpfs/pi/breaker/software/packages/cmfinder-0.4.1.18/bin
export PATH=$PATH:/gpfs/gibbs/pi/breaker/software/packages/cmfinder-0.4.1.18/bin

#################################
# Do not modify below this line
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4 changes: 2 additions & 2 deletions src/shell/infernal_source_template.sh
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Expand Up @@ -2,12 +2,12 @@
module load Infernal

# Replace with the path to the downloaded microbial igr database
DATABASE=/gpfs/ysm/pi/breaker/data/refseq98/s50.igr.fasta
DATABASE=/gpfs/gibbs/pi/breaker/data/refseq98/s50.igr.fasta

#################################
# Do not modify below this line
#################################
SEQDIR=$STEPNAME/$SEQNAME
CMBUILDCOMMAND="cmbuild -F $NOSS -o $SEQDIR/$SEQNAME.out $SEQDIR/$SEQNAME.cm $SEQDIR/$SEQNAME.sto"
CMCALIBRATECOMMAND="cmcalibrate $SEQDIR/$SEQNAME.cm"
CMSEARCHCOMMAND="cmsearch -E 0.01 -o $SEQDIR/$SEQNAME.cm.out --tblout $SEQDIR/$SEQNAME.cm.tblout -A $SEQDIR/$SEQNAME.cm.align.sto $SEQDIR/$SEQNAME.cm $DATABASE"
CMSEARCHCOMMAND="cmsearch -E 0.01 -o $SEQDIR/$SEQNAME.cm.out --tblout $SEQDIR/$SEQNAME.cm.tblout -A $SEQDIR/$SEQNAME.cm.align.sto $SEQDIR/$SEQNAME.cm $DATABASE"